Publications

Detailed Information

Contribution of Counterion Entropy to the Salt-Induced Transition Between B-DNA and Z-DNA

Cited 2 time in Web of Science Cited 3 time in Scopus
Authors

Lee, Youn Kyoung; Lee, Ju Yong; Choi, Jung Hyun; Seok, Chaok

Issue Date
2012-11
Publisher
대한화학회
Citation
Bulletin of the Korean Chemical Society, Vol.33 No.11, pp.3719-3726
Abstract
Formation of Z-DNA, a left-handed double helix, from B-DNA, the canonical right-handed double helix, occurs during important biological processes such as gene expression and DNA transcription. Such B-Z transitions can also be induced by high salt concentration in vitro, but the changes in the relative stability of B-DNA and Z-DNA with salt concentration have not been fully explained despite numerous attempts. For example, electrostatic effects alone could not account for salt-induced B-Z transitions in previous studies. In this paper, we propose that the B-Z transition can be explained if counterion entropy is considered along with the electrostatic interactions. This can be achieved by conducting all-atom, explicit-solvent MD simulations followed by MM-PBSA and molecular DFT calculations. Our MD simulations show that counterions tend to bind at specific sites in B-DNA and Z-DNA, and that more ions cluster near Z-DNA than near B-DNA. Moreover, the difference in counterion ordering near B-DNA and Z-DNA is larger at a low salt concentration than at a high concentration. The results imply that the exclusion of counterions by Z-DNA-binding proteins may facilitate Z-DNA formation under physiological conditions.
ISSN
0253-2964
URI
https://hdl.handle.net/10371/201543
DOI
https://doi.org/10.5012/bkcs.2012.33.11.3719
Files in This Item:
There are no files associated with this item.
Appears in Collections:

Related Researcher

  • Graduate School of Convergence Science & Technology
  • Dept. of Molecular and Biopharmaceutical Sciences
Research Area AI models for drug discovery, Free energy calculation, Molecular dynamics, 분자동역학, 신약개발을 위한 AI 모델, 자유에너지 계산

Altmetrics

Item View & Download Count

  • mendeley

Items in S-Space are protected by copyright, with all rights reserved, unless otherwise indicated.

Share